RPS-BLAST 2.2.22 [Sep-27-2009]
Database: pdb70
24,244 sequences; 5,693,230 total letters
Searching..................................................done
Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor
[Candidatus Liberibacter asiaticus str. psy62]
(186 letters)
>1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A
{Thermus thermophilus} SCOP: d.67.3.1 PDB: 2qbe_6 2qbg_6
2qbi_6* 2qbk_6* 2v46_Y* 2v48_Y* 2z4l_6* 2z4n_6*
Length = 185
Score = 215 bits (550), Expect = 4e-57
Identities = 78/178 (43%), Positives = 113/178 (63%)
Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
+ M ++ L+ ++ LRTGR +P++L +KVE YG+HVPLNQ+A VT +PR L
Sbjct: 7 YAETRSHMQKSLEVLEHNLAGLRTGRANPALLLHLKVEYYGAHVPLNQIATVTAPDPRTL 66
Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
VV WD+ + ++E+ I +S+LGLNP +G L I +P TEERR LV+ YAE+ +
Sbjct: 67 VVQSWDQNALKAIEKAIRDSDLGLNPSNKGDALYINIPPLTEERRKDLVRAVRQYAEEGR 126
Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
+++RNIRR+ +D LKK K SED E +IQKITD I D E+K++EI+
Sbjct: 127 VAIRNIRREALDKLKKLAKELHLSEDETKRAEAEIQKITDEFIAKADQLAEKKEQEIL 184
>1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio
parahaemolyticus} SCOP: d.67.3.1
Length = 185
Score = 195 bits (497), Expect = 6e-51
Identities = 77/178 (43%), Positives = 113/178 (63%)
Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
++ ++RM ++ LK ++ +RTGR PS+L + VE YG+ PLNQVANV + R L
Sbjct: 6 KKDAQERMDKSVEALKNNLSKVRTGRAHPSLLSGISVEYYGAATPLNQVANVVAEDARTL 65
Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
++V+DKE+ VE+ I S+LGLNP+ G ++R+P+P TEERR LVK+ AE +
Sbjct: 66 AITVFDKELTQKVEKAIMMSDLGLNPMSAGTIIRVPLPPLTEERRKDLVKIVRGEAEGGR 125
Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
++VRNIRRD + LK K + SED + +IQK+TD +K ID K+KE+M
Sbjct: 126 VAVRNIRRDANNDLKALLKDKEISEDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELM 183
>1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli}
SCOP: d.67.3.1 PDB: 1ek8_A* 1zn0_A 1zn1_A 2rdo_8
Length = 185
Score = 192 bits (490), Expect = 3e-50
Identities = 73/180 (40%), Positives = 114/180 (63%)
Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
++ + RM + K + +RTGR SPS+LD + VE YG+ PL Q+A+VTV + R L
Sbjct: 6 RKDAEVRMDKCVEAFKTQISKIRTGRASPSLLDGIVVEYYGTPTPLRQLASVTVEDSRTL 65
Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
++V+D+ M +VE+ I S+LGLNP G +R+P+P TEERR L K+ AE+++
Sbjct: 66 KINVFDRSMSPAVEKAIMASDLGLNPNSAGSDIRVPLPPLTEERRKDLTKIVRGEAEQAR 125
Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186
++VRN+ RD D +K K + SED ++D+QK+TD+ IK I++ +K+ E+M F
Sbjct: 126 VAVRNVGRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF 185
>1ge9_A Ribosome recycling factor; three-helix bundle; NMR {Aquifex
aeolicus} SCOP: d.67.3.1
Length = 184
Score = 170 bits (432), Expect = 2e-43
Identities = 65/186 (34%), Positives = 109/186 (58%), Gaps = 6/186 (3%)
Query: 1 MNQVID--LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANV 58
M + ++ + + M + + K ++ LRT R S ++++ +KVE YGS VP+ Q+ +
Sbjct: 1 MIKELEDIFKEAEKDMKKAVEYYKNEIAGLRTSRASTALVEEIKVEYYGSKVPIKQLGTI 60
Query: 59 TVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVA 118
+V E +V+ VWD+ V ++E+ I E L LNP V+G V+R+ +P TEERR LV++
Sbjct: 61 SVPEHNQIVIQVWDQNAVPAIEKAIRE-ELNLNPTVQGNVIRVTLPPLTEERRRELVRLL 119
Query: 119 HAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEE 178
H E++++ VRN+RR+ + +++ SED +QK+TD I I+ E
Sbjct: 120 HKITEEARVRVRNVRREAKEMIEELE---GISEDEKKRALERLQKLTDKYIDEINKLMEA 176
Query: 179 KKKEIM 184
K+KEIM
Sbjct: 177 KEKEIM 182
>1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle,
protein synthesis; 2.15A {Mycobacterium tuberculosis}
SCOP: d.67.3.1 PDB: 1wqf_A 1wqh_A
Length = 185
Score = 165 bits (418), Expect = 8e-42
Identities = 65/178 (36%), Positives = 110/178 (61%)
Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
L + +++M ++ + D+ T+RTGR +P M + ++ YG+ P+ Q+A++ V E R++
Sbjct: 6 LFDAEEKMEKAVAVARDDLSTIRTGRANPGMFSRITIDYYGAATPITQLASINVPEARLV 65
Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
V+ ++ + ++E I S+LG+NP +G ++R+ VP+ TEERR LVK A E++K
Sbjct: 66 VIKPYEANQLRAIETAIRNSDLGVNPTNDGALIRVAVPQLTEERRRELVKQAKHKGEEAK 125
Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
+SVRNIRR M+ L + RK G+A ED V E D+ K T + ID + K+ E++
Sbjct: 126 VSVRNIRRKAMEELHRIRKEGEAGEDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELL 183
>1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta
sandwich; 2.55A {Thermotoga maritima} SCOP: d.67.3.1
PDB: 1t1m_C
Length = 185
Score = 157 bits (398), Expect = 1e-39
Identities = 74/180 (41%), Positives = 120/180 (66%)
Query: 7 LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
++ K++M T+ ++ ++ +RTG+ SP++L+ +KV+ YG P+NQ+A +++ E R L
Sbjct: 6 IKEAKEKMKRTLEKIEDELRKMRTGKPSPAILEEIKVDYYGVPTPVNQLATISISEERTL 65
Query: 67 VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
V+ WDK +++ +E+ I+ S+LGLNPI +G V+R+ P T E+R VK A E+ K
Sbjct: 66 VIKPWDKSVLSLIEKAINASDLGLNPINDGNVIRLVFPSPTTEQREKWVKKAKEIVEEGK 125
Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186
I++RNIRR+ + +K+ +K G ED LEN+IQK+TD I+ +D FE KK+EIM F
Sbjct: 126 IAIRNIRREILKKIKEDQKEGLIPEDDAKRLENEIQKLTDEFIEKLDEVFEIKKEEIMEF 185
>3lhp_S 4E10_D0_1ISEA_004_N (T93); epitope-scaffold, immune system; 2.70A
{Artificial gene} PDB: 1y69_8
Length = 123
Score = 125 bits (316), Expect = 5e-30
Identities = 27/117 (23%), Positives = 55/117 (47%), Gaps = 4/117 (3%)
Query: 68 VSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKI 127
+S K+ +++ + L+ +R P TEER +K+ AE++++
Sbjct: 9 ISDIRKDAEVRMDKAVEAFKNKLDKFKAA--VRKVFP--TEERIKDWLKIVRGEAEQARV 64
Query: 128 SVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
+VRN+ RD D K + + ++ D+QK+TD+ IK I++ + + +
Sbjct: 65 AVRNVGRDANDKAAALGKDKEINWFDISQSLWDVQKLTDAAIKKIEAALADMEAWLT 121
>1y69_8 Ribosome recycling factor; RRF; 3.33A {Deinococcus radiodurans}
Length = 113
Score = 111 bits (280), Expect = 9e-26
Identities = 37/119 (31%), Positives = 64/119 (53%), Gaps = 7/119 (5%)
Query: 68 VSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKI 127
+S K+ +++ + ++ I G TEERR L K+ AE++++
Sbjct: 2 ISDIRKDAEVRMDKCVEAFKTQISKIRTG-------GGGTEERRKDLTKIVRGEAEQARV 54
Query: 128 SVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMHF 186
+VRN+RRD D +K K + SED ++D+QK+TD+ IK I++ +K+ E+M F
Sbjct: 55 AVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF 113
>3lf9_A 4E10_D0_1IS1A_001_C (T161); epitope-scaffold, immune system; 2.00A
{Artificial gene}
Length = 121
Score = 107 bits (268), Expect = 2e-24
Identities = 33/113 (29%), Positives = 54/113 (47%), Gaps = 7/113 (6%)
Query: 72 DKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRN 131
K+ +++ + L+ + G TEERR LVK+ AE +++VRN
Sbjct: 6 KKDAQERMDKSVEALKNNLSKVRTG-------GGGTEERRKDLVKIVRGEAEGGRVAVRN 58
Query: 132 IRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
I RD + L K + + ++ +IQK+TD +K ID K+KE+M
Sbjct: 59 IARDAANDLAALGKDKEVNWFDISQALWEIQKLTDVAVKKIDEVLAAKEKELM 111
>1wih_A Mitochondrial ribosome recycling factor; structural genomics, riken
structural genomics/proteomics initiative, RSGI, unknown
function; NMR {Mus musculus} SCOP: d.67.3.1
Length = 84
Score = 97.6 bits (243), Expect = 1e-21
Identities = 26/82 (31%), Positives = 45/82 (54%), Gaps = 1/82 (1%)
Query: 31 GRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWD-KEMVASVERGIHESNLG 89
G S LD + V V LNQ+ +++ P++++V++ E A+ + I ES +
Sbjct: 1 GSSGSSGLDHITVVTADGKVALNQIGQISMKSPQVILVNMASFPECTAAAIKAIRESGMN 60
Query: 90 LNPIVEGQVLRIPVPETTEERR 111
LNP VEG ++R+P+P+ T
Sbjct: 61 LNPEVEGTLIRVPIPKVTSGPS 82
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl reductase,
beta-ketoacyl synthase, dehydratase; 4.00A
{Saccharomyces cerevisiae}
Length = 2006
Score = 34.5 bits (79), Expect = 0.013
Identities = 33/184 (17%), Positives = 50/184 (27%), Gaps = 73/184 (39%)
Query: 45 AYGS-----HVPLNQVANVTVL-------------------EPRMLVVSVWDKEMVAS-- 78
++GS VP + L EP E+V
Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPA------ELVGKFL 65
Query: 79 --VERGIHESNLGLNPIV--------EGQVLR-----------IPVPETTEERRLALVKV 117
V + S +G V E L + +TT + L+K
Sbjct: 66 GYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIK- 124
Query: 118 AHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDI---QKITDSTIKNIDS 174
Y ++ R + L ++ G A +VA I Q N D
Sbjct: 125 --NYITARIMAKRPFDKKSNSALFRAVGEGNAQ--LVA-----IFGGQG-------NTDD 168
Query: 175 FFEE 178
+FEE
Sbjct: 169 YFEE 172
Score = 33.4 bits (76), Expect = 0.031
Identities = 24/165 (14%), Positives = 44/165 (26%), Gaps = 80/165 (48%)
Query: 48 SHVPLNQVANVTVLEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETT 107
+ + T L P +L D S+E EG P P
Sbjct: 310 CY----EAYPNTSLPPSILE----D-----SLENN------------EGV----PSP--- 337
Query: 108 EERRLALVKVAHAYAEKSKISVRNIRRDGMD--------HLKKSRK-------------- 145
+S+ N+ ++ + HL ++
Sbjct: 338 ------------------MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV 379
Query: 146 SGKASEDMVASLENDIQKITDSTIKNIDSF---FEEKKKEIMH-F 186
SG + L ++K + +D F E+K + + F
Sbjct: 380 SGPPQS--LYGLNLTLRKAKAPS--GLDQSRIPFSERKLKFSNRF 420
Score = 31.8 bits (72), Expect = 0.10
Identities = 33/187 (17%), Positives = 61/187 (32%), Gaps = 62/187 (33%)
Query: 1 MNQVIDL--QNIKDRMGDTISFLKKD---MMTLRTGR----VS--PSML-----DLVKVE 44
M + +L + ++D + T S L ++L G VS P L L K +
Sbjct: 338 MLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAK 397
Query: 45 AYG----SHVPLNQVANVTVLEPRMLVVSV-WDKEMVASVERGIHESNLGLNPI-VEGQV 98
A S +P ++ R L V+ + ++ I++ +L N + +
Sbjct: 398 APSGLDQSRIPFSERK--LKFSNRFLPVASPFHSHLLVPASDLINK-DLVKNNVSFNAKD 454
Query: 99 LRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLE 158
++IPV +T DG D L+ S + +
Sbjct: 455 IQIPVYDT---------------------------FDGSD-LRVL------SGSISERI- 479
Query: 159 NDIQKIT 165
+ I
Sbjct: 480 --VDCII 484
>3jru_B Probable cytosol aminopeptidase; bacterial blight, XOO0834, PEPA,
xanthomonas oryzae PV. ORYZ KACC10331, hydrolase,
manganese; 2.60A {Xanthomonas oryzae PV}
Length = 490
Score = 29.3 bits (65), Expect = 0.61
Identities = 10/94 (10%), Positives = 30/94 (31%), Gaps = 13/94 (13%)
Query: 66 LVVSVWDKEMVASVERGIHESNLG-LNPIVE--------GQVLRIPVPETTEERRLALVK 116
+VV + + ++ + + ++ G L ++ G + R+ +V
Sbjct: 20 IVVGAFADKTLSPAAQALDSASQGRLTALLARGDVAGKTGSTTLLHDLPGVAAPRVLVVG 79
Query: 117 VAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKAS 150
+ + K V + D + + +
Sbjct: 80 L----GDAGKFGVAPYLKAIGDATRALKTGAVGT 109
>3h8g_F Cytosol aminopeptidase; cytoplasm, hydrolase, manganese,
metal-bindi protease; HET: BES; 1.50A {Pseudomonas
putida} PDB: 3h8e_A 3h8f_A*
Length = 497
Score = 27.0 bits (59), Expect = 2.5
Identities = 14/94 (14%), Positives = 35/94 (37%), Gaps = 13/94 (13%)
Query: 66 LVVSVWDKEMVASVERGIHESNLG-LNPIVE--------GQVLRIPVPETTEERRLALVK 116
LV+ V + + +V + + ++ G ++ +++ GQ L + + + R+ LV
Sbjct: 18 LVIPVGENRKLGAVAKAVDLASEGAISAVLKRGDLAGKPGQTLLLQNLQGLKAERVLLVG 77
Query: 117 VAHAYAEKSKISVRNIRRDGMDHLKKSRKSGKAS 150
+ + R R+ + A
Sbjct: 78 S----GKDEALGDRTWRKLVASVAGVLKGLNGAD 107
>3gqi_B Phospholipase C-gamma-1; phosphorylated kinase, PY-recognition,
tandem SH2 domains, ATP analog, alternative splicing,
ATP-binding; HET: PTR DVT ACP; 2.50A {Rattus norvegicus}
PDB: 2fci_A* 2pld_A 2ple_A
Length = 226
Score = 25.1 bits (54), Expect = 9.4
Identities = 6/20 (30%), Positives = 10/20 (50%)
Query: 91 NPIVEGQVLRIPVPETTEER 110
+P+ LR P+ E E+
Sbjct: 200 HPLYRKMKLRYPINEEALEK 219
Database: pdb70
Posted date: Jan 26, 2011 11:21 AM
Number of letters in database: 5,693,230
Number of sequences in database: 24,244
Lambda K H
0.316 0.131 0.355
Gapped
Lambda K H
0.267 0.0646 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,506,205
Number of extensions: 65869
Number of successful extensions: 245
Number of sequences better than 10.0: 1
Number of HSP's gapped: 239
Number of HSP's successfully gapped: 19
Length of query: 186
Length of database: 5,693,230
Length adjustment: 87
Effective length of query: 99
Effective length of database: 3,584,002
Effective search space: 354816198
Effective search space used: 354816198
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.8 bits)